A protein-protein interaction (PPI) extraction tool to BioNLP researchers. The AkaneRE system has three parts: (i) a core engine for relation extraction (RE), (ii) a pool of modules for specific solutions, and (iii) a configuration language to adapt the system to different tasks. The overall architecture of the Akane system is a pipeline, going through the steps of sentence boundary detection, tokenization, stemming, part-of-speech tagging, parsing, named entity recognition, generation of potential relations, generation of features for each relation, and finally, assignment of confidence scores and ranking of candidate relations according to whether they are truly events/interactions or not.

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AkaneRE in publication

[…] and allow for the possibility of extending to other post-translational modifications., for the detection of ppi events, we acknowledge the systems described by papanikolaou et al. (), as well as the akanere system () and suiseki (). four of these systems are currently available as stand-alone [biorat (), opendmap (), ppiextractor () and pplook ()], with two of them available when we started […]

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Department of Information Science, University of Tokyo, Tokyo, Japan; Department of Science, University of Tokyo, Tokyo, Japan; National Centre for Text Mining, University of Manchester, Manchester, UK

AkaneRE funding source(s)

This work was partially supported by the Grant-in-Aid for Specially Promoted Research (MEXT, Japan), the Genome Network Project (MEXT, Japan), and JSPS KAKENHI (21500130).